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A human Raf-responsive zinc-finger protein that binds to divergent sequences.

LZ321, a human liver cDNA, encodes a protein that bound to a Drosophila tramtrack binding site, GGTCCT. The sequence of LZ321 matched that of RREB1, a transcription factor that bound to a Ras responsive element (RRE) very different from the sequence with which we isolated LZ321. We therefore examined the binding of RREB1/LZ321 to different ligands. It bound to the GGTCCT-containing ligand and to the RRE with similar affinities (Kd50-60 nM), but did not bind to a consensus RREB1 binding site. The RREB1/LZ321 protein contains four C2H2zinc-fingers, the C-terminal two of which retained specific DNA binding to both ligands. A trimer of the GGTCCT site functioned as an enhancer in both CV-1 and H4IIE-C3 cells. Thus RREB1/LZ321 could function as a downstream activator in the Ras-Raf signaling pathway through different cis -acting elements. A longer human protein, Finb, contains RREB1/LZ321, and there are close homologs in both chicken and Drosophila, arguing that it plays important roles. The ability of transcription factors such as RREB1/LZ321 to bind diverse sequences gives them the potential to regulate previously unsuspected genes.

Animals↗

Positive selection in the egg receptor for abalone sperm lysin.

The mechanism of speciation is a central problem in evolutionary biology. In free-spawning animals with no complex mating behavior, prezygotic reproductive isolation (speciation) could result from the rapid divergence of genes coding for sperm and egg proteins that bind each other during fertilization. In abalone, sperm lysin evolves rapidly by positive Darwinian selection. The egg vitelline envelope receptor for lysin had previously been shown to evolve neutrally and be subjected to concerted evolution. Several mathematical simulations predict that both male and female reproductive proteins should evolve rapidly by positive selection. Here we report that the sequence diversity of the amino-terminal end of the egg vitelline envelope receptor for lysin has been promoted by positive Darwinian selection. These data provide molecular support for theoretical models showing that the two sexes are locked in a "coevolutionary chase" that could be driven by processes such as sexual selection, sexual conflict, or microbial attack (pathogen avoidance). The result of this continuous coevolution of the gamete recognition system could be the splitting of one population into two that are reproductively isolated (speciation).

Animals↗

DNA barcoding Korean birds.

DNA barcoding, an inventory of DNA sequences from a standardized genomic region, provides a bio-barcode for identifying and discovering species. Several recent studies suggest that the sequence diversity in a 648 bp region of the mitochondrial gene for cytochrome c oxi- dase I (COI) might serve as a DNA barcode for identify- ing animal species such as North American birds, in- sects and fishes. The present study tested the effective- ness of a COI barcode in discriminating Korean bird species. We determined the 5' terminus of the COI bar- code for 92 species of Korean birds and found that spe- cies identification was unambiguous; the genetic differ- ences between closely related species were, on average, 25 times higher than the differences within species. We identified only one misidentified species out of 239 specimens in a genetic resource bank, so confirming the accuracy of species identification in the banking system. We also identified two potential composite species, calling for further investigation using more samples. The finding of large COI sequence differences between species confirms the effectiveness of COI barcodes for identifying Korean bird species. To bring greater reliability to the identification of species, increased in- tra- and interspecies sampling, as well as supplementa- tion of the mitochondrial barcodes with nuclear ones, is needed.

Animals↗

DNA shuffling as a tool for protein crystallization.

The success of structural studies performed on an individual target in small scale or on many targets in the system-wide scale of structural genomics depends critically on three parameters: (i) obtaining an expression system capable of producing large quantities of the macromolecule(s) of interest, (ii) purifying this material in soluble form, and (iii) obtaining diffraction-quality crystals suitable for x-ray analysis. The attrition rate caused by these constraints is often quite high. Here, we present a strategy that addresses each of these three parameters simultaneously. Using DNA shuffling to introduce functional sequence variability into a protein of interest, we screened crude lysate supernatants for soluble variants that retain enzymatic activity. Crystallization trials performed on three WT and eight shuffled enzymes revealed two variants that crystallized readily. One of these was used to determine the high-resolution structure of the enzyme by x-ray analysis. The sequence diversity introduced through shuffling efficiently samples crystal packing space by modifying the surface properties of the enzyme. The approach demonstrated here does not require guidance as to the type of mutation necessary for improvements in expression, solubility, or crystallization. The method is scaleable and can be applied in situations where a single protein is being studied or in high-throughput structural genomics programs. Furthermore, it should be readily applied to structural studies of soluble proteins, membrane proteins, and macromolecular complexes.

Acetyltransferases↗

Cloning and biological characterization of human single-chain Fv fragments that mediate neutralization of HIV-1.

OBJECTIVE: To develop recombinant single-chain Fv fragments against HIV-1 gp120. METHODS: A panel of human monoclonal antibody Fv fragments were generated against the HIV-1 gp120 by affinity selection from an antibody library expressed on the surface of filamentous phage. The library was prepared from peripheral blood lymphocytes of an asymptomatic HIV-1-infected mother with a high neutralization titer. This mother did not transmit HIV-1 to her offspring (non-transmitter). Heavy and light chains were initially amplified separately and combined by splicing by overlap extension to generate Fv fragments. RESULTS: Several clones expressing single-chain Fv fragments bind strongly to HIV-1 gp120 and several were found to neutralize cell-free HIV-1IIIB. Gross epitope mapping suggest that different clones bound to different functional regions on the envelope. The clones also exhibited sequence diversity. CONCLUSIONS: This strategy of cloning resulted in the development of functional human-derived antibody reagents with different anti-HIV-1 biological properties in vitro. These recombinant Fv fragments have potential utility as immune reagents, as well as in the design of potential immunotherapeutics. In addition, these antibody reagents may provide information on the relationship between humoral immunity and maternal-fetal (vertical) HIV-1 transmission.

Acquired Immunodeficiency Syndrome↗

Secondary structure of the 3'-noncoding region of flavivirus genomes: comparative analysis of base pairing probabilities.

The prediction of the complete matrix of base pairing probabilities was applied to the 3' noncoding region (NCR) of flavivirus genomes. This approach identifies not only well-defined secondary structure elements, but also regions of high structural flexibility. Flaviviruses, many of which are important human pathogens, have a common genomic organization, but exhibit a significant degree of RNA sequence diversity in the functionally important 3'-NCR. We demonstrate the presence of secondary structures shared by all flaviviruses, as well as structural features that are characteristic for groups of viruses within the genus reflecting the established classification scheme. The significance of most of the predicted structures is corroborated by compensatory mutations. The availability of infectious clones for several flaviviruses will allow the assessment of these structural elements in processes of the viral life cycle, such as replication and assembly.

Algorithms↗

Multiplicity of macrolide-lincosamide-streptogramin antibiotic resistance determinants.

Bacteria can resist macrolide, lincosamide, and streptogramin (MLS) antibiotics enzymically by alteration of the target site or detoxification of the antibiotic. N6-dimethylation of adenine in 23 S ribosomal RNA confers resistance to M, L, and S B-type (MLSB) antibiotics. Investigation, by DNA annealing, of the relationship between the genes specifying this resistance mechanism from Streptococcus (groups A,B,D, and H, and pneumoniae), Staphylococcus aureus, Bacillus licheniformis, Bacteroides fragilis, Lactobacillus casei, and Streptomyces erythreus indicated substantial sequence diversity among the MLSB resistance (R) determinants. A minimum of four distinct classes of MLSB R determinants could be defined: classes A and B for the Gram-positive cocci (streptococci pmeumococci and staphylococci), class C for B. licheniformis, and class D for Bact. fragilis. These data do not support the hypothesis that the R determinants were acquired recently from a single common origin and suggest an easy exchange of genetic information among the Gram-positive cocci. The genetic classes do not correlate with differences in phenotypic expression or in regulation (inducibility or constitutivity) of resistance towards MLSB antibiotics. Inactivation of the drug confers resistance to M and/or L and/or S or SA or SB antibiotics and has been detected in strains of Streptococcus, Staph. aureus, Lactobacillus, C. perfringens, Streptomyces, and recently in the Gram-negative organism Escherichia coli. We have cloned and sequenced a DNA fragment conferring high level resistance (MIC greater than 2 g/l) to erythromycin by hydrolysis of the antibiotic. The distribution of this 'new' character in enterobacteria isolated from human faeces was studied by colony hybridization using an intragenic probe. The gene for the erythromycin esterase was detected in numerous strains of E. coli belonging to various biotypes, in Klebsiella pneumoniae, Enterobacter agglomerans, and in one 'coliform'. Moreover, our results indicated the existence of at least two classes of genes specifying resistance to erythromycin by inactivation of the antibiotic in enterobacteria.

Anti-Bacterial Agents↗

Sequence variation of human papillomavirus type 16 E7 in preinvasive and invasive cervical neoplasias.

Variation in the nucleotide sequence of the HPV 16 E7 gene in preinvasive cervical intraepitherial neoplasia (CIN) and invasive cervical carcinoma specimens was analyzed. Direct DNA sequencing of PCR-amplified products with primers different from those used for PCR with 5'-end labeling generated distinct sequence ladders with a low background, even in specimens containing relatively low copy numbers of HPV. Of 14 cervical neoplasias, 11 cases showed sequence diversity from prototype HPV16, and a total of 22 nucleotide exchanges were detected. Nine of these led to single amino acid exchanges: [Thr5] to [Lys5] in one case and [Asn29] to [Ser29] in eight cases. The [Ser29] E7 was distributed uniformly among invasive carcinomas and precancerous legions, and was also found in a normal cervix. The [Lys5] E7 and [Ser29] E7 had transforming potential similar to the prototype E7 assessed by cooperation with the activated ras gene in rat embryo fibroblasts.

Amino Acid Sequence↗

Vaccinia virus encodes two proteins that are structurally related to members of the plasma serine protease inhibitor superfamily.

Nucleotide sequencing adjacent to the right inverted terminal repetition of the vaccinia virus genome revealed two genes encoding polypeptides that are structurally related to members of the plasma serine protease inhibitor superfamily (SPI). Inclusion in the superfamily is based on extensive amino acid sequence similarities as well as a consensus sequence adjacent to the active-site region near the carboxyl ends of the proteins. The genes designated SPI-1 and SPI-2 are located 10,000 and 17,000 base pairs from the right end of the genome, respectively. The predicted SPI-1 polypeptide is 11 amino acids longer than that of SPI-2, and the deduced masses are 40,471 and 38,125 daltons, respectively. Similarities between SPI-1 and SPI-2 are indicated by the percentage of identical amino acids (44%) and corresponding hydrophobicity plots. The maximum amino acid sequence diversity occurs precisely in the putative active-site region, suggesting that SPI-1 and SPI-2 may inhibit different proteases. SPI-2 is homologous to a previously described cowpox virus gene (D. J. Pickup, B. S. Ink, W. Hu, C. A. Ray, and W. K. Joklik, Proc. Natl. Acad. Sci. USA 83:7698-7702, 1986). Evidence for a cowpox virus homolog of SPI-1 was obtained by DNA hybridization. Thus, the presence of two genes that belong to the plasma serine protease inhibitor superfamily may be characteristic of orthopoxviruses.

Amino Acid Sequence↗

The role of VL gene structural determinants in the fine specificity of anti-DNA antibodies.

To investigate the structural contribution of the light chain of anti-DNA antibodies to fine specificity, the VKappa genes of two monoclonal anti-DNA antibodies, termed H241 and H102, were cloned and sequenced. H102 and H241 are independently derived from MRL-lpr/lpr mice and differ in their fine specificity: H241 binds dsDNA and normal glomeruli in vitro and deposits in the kidney in vivo, whereas H102 binds only ssDNA and does not deposit in the kidney. Both are encoded by nearly identical VH genes but different N and D regions. Our previous results have demonstrated that the VH gene for H102 and H241 encodes eight other anti-DNA antibodies that also differed in fine specificity. This suggested that the gene product encoded by the VH 102/241 gene, may have intrinsic affinity for DNA, but is unlikely to determine fine specificity or nephritogenicity. In the present study we examined whether the VKappa gene might account for the difference in nephritogenicity. The complete nucleotide and deduced amino acid sequence of VK 102 and VK241 revealed that they are very dissimilar to each other (< 60% homology). VK 241 defined a new member of the VKappa gene family and was moderately homologous to two other VK genes encoding anti-DNA antibodies and to one VK gene encoding an anti-histone antibody all from lupus strains of mice. In addition, sequence diversity in the VK CDR1 region and position 96 of the CDR3 region was observed that may be of significance in determining fine specificity. VK 102 was highly homologous to two other VKappa genes, VKs17.2 and VK C8.5, both encoding anti-DNA antibodies and members of the VK20 gene family. It was striking that all three members of the VK 20 gene family code for DNA reactivity. This suggests that certain VKappa genes may also be used to repeatedly code for anti-DNA reactivity.

Amino Acid Sequence↗

Sequence analysis of the beta-giardin gene and development of a polymerase chain reaction-restriction fragment length polymorphism assay to genotype Giardia duodenalis cysts from human faecal samples.

The flagellate parasite Giardia duodenalis is a major cause of diarrhoea in humans and in animals worldwide. Molecular techniques are particularly useful for studying the taxonomy, the population structure, the zoonotic potential of animal isolates, and the correlation between the genetic variability of the parasite and the range of clinical symptoms observed in humans. In this work, a new PCR assay that targets the beta-giardin gene was tested on 21 Giardia duodenalis reference strains representing Assemblages A, B and E, which are associated with infections of humans and other mammals. The assay was then applied to 30 faecal samples collected from Italian persons. The sequence analysis of 31 PCR products from both reference strains and clinical samples showed that each Assemblage is clearly distinct from the others on the basis of specific substitutions; the sequence diversity was approximately 5%, and all substitutions occurred at the third codon positions of the gene. The analysis of the intra-Assemblage variability allowed for the identification of three genotypes within Assemblage A, and of four genotypes within Assemblage B. Interestingly, two genotypes were identified only in the clinical samples and not in reference strains. Finally, a simple PCR-restriction fragment length polymorphism method was developed for the rapid discrimination of Assemblages and applied for the direct genetic analysis of cysts present in human faecal samples.

Animals↗

Stage-specific expression of aldolase isoenzymes in the rodent malaria parasite Plasmodium berghei.

We have cloned two gene (aldo-1 and aldo-2) encoding the glycolytic enzyme aldolase of the rodent malaria parasite Plasmodium berghei. The amino acid sequence of one gene product, ALDO-1, is virtually identical to P. falciparum aldolase whereas ALDO-2, the second gene product, is different and has 13% sequence diversity to ALDO-1. We expressed ALDO-2 as an active enzyme in Escherichia coli and compared the biochemical and kinetic properties to that of P. falciparum recombinant aldolase (ALDO-1 type). Based on the Km and Vmax constants for FMP and FBP, neither ALDO-1 nor ALDO-2 can be clearly assigned to any of the known mammalian isoenzyme classes. We demonstrate that expression of the two isoenzymes is developmentally regulated: specific antibody probes detect ALDO-1 in sporozoite stages of P. berghei and ALDO-2 is found in blood stage parasites.

Amino Acid Sequence↗

A recent common ancestry for human Y chromosomes.

The male-specific portion of the Y chromosome is especially useful for studies of human origins. Patterns of nucleotide variation that are neutral with respect to fitness should permit estimates of when and where ancestral Y chromosomes existed. However, variation on the human Y chromosome has been observed to be greatly reduced relative to the autosomes and the X chromosome. One explanation is that selection for a favourable mutation on the non-recombining portion of the Y chromosome has resulted in the recent fixation of a single Y haplotype. A 2.6-kilobase fragment encompassing a polymorphic Alu insertion was sequenced from 16 human and four chimpanzee Y chromosomes. Patterns of nucleotide sequence diversity and divergence provide no evidence for a recent, strong selective sweep on the human Y chromosome. The time back to a common ancestral human Y chromosome is estimated to be 188,000 years, with a 95% confidence interval from 51,000 to 411,000 years. These results are consistent with autosomal and mitochondrial DNA studies that suggest a long-term human effective population size of 10,000 and a sex ratio of 1 (ref. 7). These inferences contradict predictions of the multiregional hypothesis positing a widespread transformation of Homo erectus populations into Homo sapiens.

Animals↗

Detection of small round structured viruses in shellfish by reverse transcription-PCR.

We describe the application of a previously developed sample extraction procedure to the detection of small round structured viruses (SRSVs) in shellfish. Initial seeding experiments showed that PCR inhibitor removal and virus recoveries were comparable to those in previous studies with poliovirus. Shellfish from a range of sewage-contaminated sites were then tested for the presence of SRSVs by using broadly reactive PCR primers followed by Southern blotting with internal probe sites. Positive results were obtained from 5 of 31 field samples tested. Four of these positive samples were from highly polluted sites. PCR product sequence analysis confirmed their identity as SRSV and showed sequence diversity compared with virus controls, suggesting that the results were not a consequence of PCR cross-contamination. Finally, shellfish associated with four separate outbreaks of viral gastroenteritis were tested by PCR and Southern blot for the presence of SRSVs. All outbreak samples tested gave positive results. As far as we are aware, this is the first demonstration of the detection in environmentally contaminated shellfish of the SRSVs responsible for human gastroenteritis. This development may help contribute to the further development of public health controls for molluscan shellfish.

Amino Acid Sequence↗

Population structure of the Bacillus cereus group as determined by sequence analysis of six housekeeping genes and the plcR Gene.

The population structure of the Bacillus cereus group (52 strains of B. anthracis, B. cereus, and B. thuringiensis) was investigated by sequencing seven gene fragments (rpoB, gyrB, pycA, mdh, mbl, mutS, and plcR). Most of the strains were classifiable into two large subgroups in six housekeeping gene trees but not in the plcR tree. In addition, several consistent clusters were identified, which were unrelated to species distinction. Moreover, interrelationships among these clusters were incongruent in each gene tree. The incongruence length difference test and split decomposition analyses also showed incongruences between genes, suggesting horizontal gene transfer. The plcR gene was observed to have characteristics that differed from those of the other genes in terms of phylogenetic topology and pattern of sequence diversity. Thus, we suggest that the evolutionary history of the PlcR regulon differs from those of the other chromosomal genes and that recombination of the plcR gene may be frequent. The homogeneity of B. anthracis, which is depicted as an independent lineage in phylogenetic trees, is suggested to be of recent origin or to be due to the narrow taxonomic definition of species.

Animals↗

Origin and evolution of genes specifying resistance to macrolide, lincosamide and streptogramin antibiotics: data and hypotheses.

Resistance to macrolide, lincosamide and streptogramin antibiotics is due to alteration of the target site or detoxification of the antibiotic. Postranscriptional methylation of 23S ribosomal rRNA confers resistance to macrolide (M), lincosamide (L) and streptogramin (S) B-type antibiotics, the so-called MLSB phenotype. Several classes of rRNA methylases conferring resistance to MLSB antibiotics have been characterized in Gram-positive cocci, in Bacillus spp, and in strains of actinomycetes producing erythromycin. The enzymes catalyze N6-dimethylation of an adenine residue situated in a highly conserved region of prokaryotic 23S rRNA. In this review, we compare the amino acid sequences of the rRNA methylases and analyze the codon usage in the corresponding erm (erythromycin resistance methylase) genes. The homology detected at the protein level is consistent with the notion that an ancestor of the erm genes was implicated in erythromycin resistance in a producing strain. However, the rRNA methylases of producers and non-producers present substantial sequence diversity. In Gram-positive bacteria the preferential codon usage in the erm genes reflects the guanosine plus cytosine content of the chromosome of the host. These observations suggest that the presence of erm genes in these micro-organisms is ancient. By contrast, it would appear that enterobacteria have acquired only recently an rRNA methylase gene of the ermB class from a Gram-positive coccus since the genes isolated in Escherichia coli and in Gram-positive cocci are highly homologous (homology greater than 98%) and present a codon usage typical of the latter micro-organisms. As opposed to the MLSB phenotype which results from a single biochemical mechanism, inactivation of structurally related antibiotics of the MLS group involves synthesis of various other enzymes. In enterobacteria, resistance to erythromycin and oleandomycin is due to production of erythromycin esterases which hydrolyze the lactone ring of the 14-membered macrolides. We recently reported the nucleotide sequence of ereA and ereB (erythromycin resistance esterase) genes which encode erythromycin esterases type I and II, respectively. The amino acid sequences of the two isozymes do not exhibit statistically significant homology. Analysis of codon usage in both genes suggests that esterase type I is indigenous to E. coli, whereas the type II enzyme was acquired by E. coli from a phylogenetically remote micro-organism. Inactivation of lincosamides, first reported in staphylococci and lactobacilli of animal origin, was also recently detected in Gram-positive cocci isolated from humans.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

Topology of outer membrane porins in pathogenic Neisseria spp.

In Escherichia coli, membrane-spanning amphipathic beta-sheet structures are characteristic of many outer membrane proteins. By applying the principles that have been recognized for them to the four classes of neisserial porins, we have constructed a model for the topology of the porins within the outer membrane. This model predicts eight surface-exposed loops, both in the meningococcal class 1 and 2 proteins and in the gonococcal PIA and PIB proteins. The transmembrane sequences are highly conserved among these porins and are able to form an amphipathic beta-sheet structure. The surface-exposed hydrophilic loops show extensive variation in both length and sequence. Experimental evidence in support of this model has been obtained by using antisera against synthetic peptides which correspond to surface-exposed loops in class 1 and 2 proteins. Thus, binding to the cell surface was observed with antibodies against loops 1, 4, and 5 of class 1 and loops 1 and 5 of class 2. In class 1, these loops are the longest ones and show the highest sequence diversity among strains of different subtypes. Mapping of epitopes recognized by monoclonal antibodies with bactericidal activity has also provided strong support for the model. The epitopes are located in loops 1 and 4 of class 1 protein, loop 5 of PIB, and loop 6 of PIA. A nonbactericidal antibody that binds only weakly to whole cells was shown to recognize loop 3 of PIB. These results suggest that the longest loops are immunodominant, provide the binding sites for bactericidal antibodies, and display the greatest variation among different strains.

Amino Acid Sequence↗

Analysis of CD4(+) T-cell responses to human papillomavirus (HPV) type 11 L1 in healthy adults reveals a high degree of responsiveness and cross-reactivity with other HPV types.

Human papillomavirus type 11 (HPV-11) infection causes genital warts and recurrent respiratory papillomatosis. While there is compelling evidence that CD4(+) T cells play an important role in immune surveillance of HPV-associated diseases, little is known about human CD4(+) T-cell recognition of HPV-11. We have investigated the CD4(+) T-cell responses of 25 unrelated healthy donors to HPV-11 L1 virus-like particles (VLP). CD4(+) T-cell lines from 21 of 25 donors were established. Cell sorting experiments carried out on cells from six donors demonstrated that the response was located in the CD45RA(low) CD45RO(high) memory T-cell population. To determine the peptide specificity of these responses, epitope selection was analyzed by using 95 15-mer peptides spanning the entire HPV-11 L1 protein. No single region of L1 was immunodominant; responders recognized between 1 and 10 peptides, located throughout the protein, and peptide responses fell into clear HLA class II restricted patterns. Panels of L1 peptides specific for skin and genital HPV were used to show that the L1 CD4(+) T-cell responses were cross-reactive. The degree of cross-reactivity was inversely related to the degree of L1 sequence diversity between these viruses. Finally, responses to HPV-11 L1 peptides were elicited from ex vivo CD45RO(+) peripheral blood mononuclear cells, demonstrating that recognition of HPV-11 was a specific memory response and not due to in vitro selection during tissue culture. This is the first study of CD4(+) T-cell responses to HPV-11 in healthy subjects and demonstrates marked cross-reactivity with other skin and genital HPV types. This cross-reactivity may be of significance for vaccine strategies against HPV-associated clinical diseases.

Amino Acid Sequence↗